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DNMT3A Mutation Analysis Test

Last updated July 26, 2019

Approved by: Krish Tangella MD, MBA, FCAP

The DNMT3A Mutation Analysis Test is a genetic test to detect abnormalities in the DNMT3A gene. It also aids in the treatment of leukemia by guiding selection of therapeutic drugs, including disqualifying certain drugs from being used.

What are other Names for this Test? (Equivalent Terms)

  • DNA (Cytosine-5-)-Methyltransferase 3 Alpha Mutation Analysis Test
  • DNA MTase HsaIIIA Mutation Analysis Test
  • DNMT3A2 Mutation Analysis Test

What is DNMT3A Mutation Analysis Test? (Background Information)

  • DNMT3A mutation refers to an alteration in the DNMT3A gene, which is associated with white blood cell cancer (leukemia)
  • The DNMT3A gene gives instructions for a protein called DNA methyltransferase 3 alpha. As its name implies, the role of this important protein is to chemically modify, via methylation, the DNA in cells
  • Methylation of DNA allows cells to control which parts of its genome will be converted into protein. Whether or not a region of DNA is methylated may have widespread effects on the growth and division of the cell
  • Early blood cells, in particular, use DNMT3A to regulate their development into mature blood cells - the red blood cells (erythrocytes) and white blood cells (leukocytes)
  • Abnormalities in the DNMT3A gene may result in a defective DNMT3A protein. Unable to properly methylate their DNA, early white blood cells are left to grow and divide uncontrollably into abnormal white blood cells
  • The result of this uncontrolled growth and division of leukocytes may lead to the following white blood cell cancers:
    • Cytogenetically normal acute myeloid leukemia (CN-AML): CN-AML is a rare form of white blood cell cancer
    • T-cell acute lymphoblastic leukemia
  • The DNMT3A Mutation Analysis Test is a genetic test to detect abnormalities in the DNMT3A gene. It also aids in the treatment of leukemia by guiding selection of therapeutic drugs, including disqualifying certain drugs from being used

The molecular testing, in general, can be performed using a variety of methods. Some of these methods include:

  • In situ hybridization technique, such as fluorescence in situ hybridization (FISH)
  • Immunohistochemistry (IHC)
  • Next-generation sequencing (NGS)
  • Polymerase chain reaction (PCR)
  • Comparative genomic hybridization (CGH)
  • Karyotyping including spectral karyotyping
  • mRNA analysis
  • Tissue microarrays (TMAs)
  • Southern blot test
  • Northern blot test
  • Western blot test
  • Eastern blot test

The methodology used for the test may vary from one laboratory to another. 

Note: Molecular testing has limitations due to the molecular method and genetic mutational abnormalities being tested. This can affect the results on a case-by-case basis. Consultation with your healthcare provider will help in determining the right test and right molecular method, based on individual circumstances.

What are the Clinical Indications for performing the DNMT3A Mutation Analysis Test?

Following are the clinical indications for performing the DNMT3A Mutation Analysis Test:

  • Fever
  • Bone pain
  • Lethargy and fatigue
  • Shortness of breath
  • Pale skin
  • Frequent infections
  • Easy bruising
  • Unusual bleeding, such as frequent nosebleeds and bleeding from the gums

In general, the molecular genetic testing is undertaken in the following situations:

  • To assist (and in some cases, confirm) the initial diagnosis
  • To distinguish other tumors/conditions that have similar histological features, when examined by a pathologist under the microscope
  • To help in determining treatment options
  • To confirm recurrence of the tumor: Tumor recurrence can either be at the original tumor site, or at a distant location (away from the initial site)

How is the Specimen Collected for DNMT3A Mutation Analysis Test?

Following is the specimen collection process for DNMT3A Mutation Analysis Test:

The specimen sample requirements may vary from lab to lab. Hence, it is important to contact the testing lab for exact specimen requirements, before initiating the testing process.

  • Sample on which the test is performed may include:
    • Fresh tumor tissue during biopsy
    • Formalin-fixed paraffin-embedded solid tumor tissue (FFPE tumor tissue), often referred to as paraffin block of the tumor
    • Unstained tissue slides
  • Process of obtaining the sample: As outlined by the laboratory testing facility
  • Preparation required: As outlined by the laboratory testing facility


  • In some cases, a different source of specimen (such as peripheral blood, bone marrow biopsy specimen, or other body fluids) may be acceptable to the laboratory performing the test
  • Occasionally, additional samples may be required to either repeat the test or to perform follow-up testing
  • Depending on the location of testing, it may take up to 2 weeks’ turnaround time, to obtain the test results
  • Many hospitals preserve the paraffin blocks for at least 7 years. In general, older paraffin blocks (over 5 years) may affect the detection of specific mutations, due to degradation of the tumor specimen over time

Cost of DNMT3A Mutation Analysis Test:

  • The cost of the test procedure depends on a variety of factors, such as the type of your health insurance, annual deductibles, co-pay requirements, out-of-network and in-network of your healthcare providers and healthcare facilities
  • In many cases, an estimate may be provided before the test is conducted. The final amount may depend upon the findings during the test procedure and post-operative care that is necessary (if any)

What is the Significance of the DNMT3A Mutation Analysis Test Result?

A mutation in the DNMT3A gene indicates a positive result for the DNMT3A Mutation Analysis Test. This may point to a diagnosis of:

  • Cytogenetically normal acute myeloid leukemia (CN-AML)
  • T-cell acute lymphoblastic leukemia

The laboratory test results are NOT to be interpreted as results of a "stand-alone" test. The test results have to be interpreted after correlating with suitable clinical findings and additional supplemental tests/information. Your healthcare providers will explain the meaning of your tests results, based on the overall clinical scenario.

Additional and Relevant Useful Information:

  • DNMT3A mutation most notably occurs in a location of the chromosome called 2p23.3 - i.e., the short arm (p) of chromosome 2 in position 23.3
  • Many laboratories may not have the capability to perform this test. Only highly-specialized labs with advanced facilities and testing procedures may perform this test

Certain medications that you may be currently taking may influence the outcome of the test. Hence, it is important to inform your healthcare provider of the complete list of medications (including any herbal supplements) you are currently taking. This will help the healthcare provider interpret your test results more accurately and avoid unnecessary chances of a misdiagnosis.

The following DoveMed website link is a useful resource for additional information:


Please visit our Laboratory Procedures Center for more physician-approved health information:


References and Information Sources used for the Article:

Helpful Peer-Reviewed Medical Articles:

Reviewed and Approved by a member of the DoveMed Editorial Board
First uploaded: Feb. 1, 2017
Last updated: July 26, 2019